[2024-01-25 20:00:05,633] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:00:05,634] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:00:05,634] [INFO] DQC Reference Directory: /var/lib/cwl/stg29a0b9ef-2a2e-4321-a388-807c0b12be17/dqc_reference
[2024-01-25 20:00:06,726] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:00:06,727] [INFO] Task started: Prodigal
[2024-01-25 20:00:06,727] [INFO] Running command: gunzip -c /var/lib/cwl/stg78d8ba83-3a14-4cb7-8fb7-e886e5eda3e1/GCF_030409215.1_ASM3040921v1_genomic.fna.gz | prodigal -d GCF_030409215.1_ASM3040921v1_genomic.fna/cds.fna -a GCF_030409215.1_ASM3040921v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:00:17,524] [INFO] Task succeeded: Prodigal
[2024-01-25 20:00:17,524] [INFO] Task started: HMMsearch
[2024-01-25 20:00:17,524] [INFO] Running command: hmmsearch --tblout GCF_030409215.1_ASM3040921v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29a0b9ef-2a2e-4321-a388-807c0b12be17/dqc_reference/reference_markers.hmm GCF_030409215.1_ASM3040921v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:00:17,760] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:00:17,761] [INFO] Found 6/6 markers.
[2024-01-25 20:00:17,797] [INFO] Query marker FASTA was written to GCF_030409215.1_ASM3040921v1_genomic.fna/markers.fasta
[2024-01-25 20:00:17,797] [INFO] Task started: Blastn
[2024-01-25 20:00:17,797] [INFO] Running command: blastn -query GCF_030409215.1_ASM3040921v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29a0b9ef-2a2e-4321-a388-807c0b12be17/dqc_reference/reference_markers.fasta -out GCF_030409215.1_ASM3040921v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:18,684] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:18,686] [INFO] Selected 21 target genomes.
[2024-01-25 20:00:18,687] [INFO] Target genome list was writen to GCF_030409215.1_ASM3040921v1_genomic.fna/target_genomes.txt
[2024-01-25 20:00:18,702] [INFO] Task started: fastANI
[2024-01-25 20:00:18,702] [INFO] Running command: fastANI --query /var/lib/cwl/stg78d8ba83-3a14-4cb7-8fb7-e886e5eda3e1/GCF_030409215.1_ASM3040921v1_genomic.fna.gz --refList GCF_030409215.1_ASM3040921v1_genomic.fna/target_genomes.txt --output GCF_030409215.1_ASM3040921v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:39,308] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:39,308] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29a0b9ef-2a2e-4321-a388-807c0b12be17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:39,308] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29a0b9ef-2a2e-4321-a388-807c0b12be17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:39,320] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:00:39,321] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:00:39,321] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	87.1843	836	1360	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	86.6711	863	1360	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	85.8986	895	1360	95	below_threshold
Halomonas alimentaria	strain=DSM 15356	GCA_009902005.1	147248	147248	type	True	85.8981	775	1360	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	85.8465	927	1360	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	85.8207	952	1360	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	85.5276	868	1360	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	85.3394	944	1360	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	84.8557	816	1360	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	84.6689	850	1360	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	84.6185	830	1360	95	below_threshold
Halomonas cerina	strain=CECT 7282	GCA_014192215.1	447424	447424	type	True	84.232	871	1360	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	84.1053	869	1360	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	84.0005	817	1360	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	83.7651	838	1360	95	below_threshold
Halomonas gudaonensis	strain=CGMCC 1.6133	GCA_900100195.1	376427	376427	type	True	83.3357	809	1360	95	below_threshold
Halomonas halodenitrificans	strain=DSM 735	GCA_000620045.1	28252	28252	type	True	83.3063	709	1360	95	below_threshold
Halomonas icarae	strain=D1-1	GCA_009901955.1	2691040	2691040	type	True	83.2873	769	1360	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	82.8107	807	1360	95	below_threshold
Halomonas salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	82.726	832	1360	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	82.496	812	1360	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:00:39,322] [INFO] DFAST Taxonomy check result was written to GCF_030409215.1_ASM3040921v1_genomic.fna/tc_result.tsv
[2024-01-25 20:00:39,322] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:39,323] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:39,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29a0b9ef-2a2e-4321-a388-807c0b12be17/dqc_reference/checkm_data
[2024-01-25 20:00:39,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:39,365] [INFO] Task started: CheckM
[2024-01-25 20:00:39,366] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409215.1_ASM3040921v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409215.1_ASM3040921v1_genomic.fna/checkm_input GCF_030409215.1_ASM3040921v1_genomic.fna/checkm_result
[2024-01-25 20:01:14,853] [INFO] Task succeeded: CheckM
[2024-01-25 20:01:14,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:01:14,874] [INFO] ===== Completeness check finished =====
[2024-01-25 20:01:14,874] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:01:14,874] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409215.1_ASM3040921v1_genomic.fna/markers.fasta)
[2024-01-25 20:01:14,874] [INFO] Task started: Blastn
[2024-01-25 20:01:14,874] [INFO] Running command: blastn -query GCF_030409215.1_ASM3040921v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29a0b9ef-2a2e-4321-a388-807c0b12be17/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409215.1_ASM3040921v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:16,490] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:16,492] [INFO] Selected 19 target genomes.
[2024-01-25 20:01:16,493] [INFO] Target genome list was writen to GCF_030409215.1_ASM3040921v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:01:16,502] [INFO] Task started: fastANI
[2024-01-25 20:01:16,503] [INFO] Running command: fastANI --query /var/lib/cwl/stg78d8ba83-3a14-4cb7-8fb7-e886e5eda3e1/GCF_030409215.1_ASM3040921v1_genomic.fna.gz --refList GCF_030409215.1_ASM3040921v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409215.1_ASM3040921v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:01:34,194] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:34,206] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:01:34,206] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_900104135.1	s__Halomonas shengliensis	87.1589	836	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCF_014193375.1	s__Halomonas campaniensis	86.7003	861	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182195.1	s__Halomonas sp003182195	86.3586	750	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.47	95.24	0.85	0.84	3	-
GCA_018401555.1	s__Halomonas sp018401555	86.2541	725	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202205.1	s__Halomonas sp003202205	86.1719	989	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009902005.1	s__Halomonas alimentaria	85.9297	772	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363555.1	s__Halomonas ventosae	85.8982	895	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.59	95.59	0.89	0.89	2	-
GCF_002879645.1	s__Halomonas heilongjiangensis	85.8581	925	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
GCA_014859505.1	s__Halomonas sp014859505	85.72	708	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056305.1	s__Halomonas denitrificans	85.5279	868	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363755.1	s__Halomonas sp009363755	85.3541	825	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003552795.1	s__Halomonas sp003552795	85.3165	582	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886615.1	s__Halomonas aestuarii	84.853	816	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002549795.1	s__Halomonas beimenensis	84.7329	845	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192215.1	s__Halomonas cerina	84.2518	869	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254665.1	s__Halomonas lactosivorans	84.1195	867	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100195.1	s__Halomonas gudaonensis	83.3228	809	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620045.1	s__Halomonas halodenitrificans	83.283	710	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.15	97.15	0.89	0.89	2	-
GCF_002286975.1	s__Halomonas_B sp002286975	82.7113	832	1360	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:01:34,207] [INFO] GTDB search result was written to GCF_030409215.1_ASM3040921v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:01:34,208] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:01:34,211] [INFO] DFAST_QC result json was written to GCF_030409215.1_ASM3040921v1_genomic.fna/dqc_result.json
[2024-01-25 20:01:34,211] [INFO] DFAST_QC completed!
[2024-01-25 20:01:34,211] [INFO] Total running time: 0h1m29s